Abstract Programmed or unintentional RNA cleavage leads to "dirty" RNA 5´ and 3´ ends that are remodeled by RNA end modification enzymes. The products of RNA end modification are substrates for RNA processing activities that catalyze RNA repair, decay or stabilization. Because some processing enzymes recognize different modified termini, RNA end modification enzymes could promote some processing steps while inhibiting others. Conversely, RNA processing enzymes that catalyze different reactions might recognize – and compete for – substrates with the same end modification to control the outcome of RNA cleavage. These different scenarios could potentially be used to regulate the outcome of RNA cleavage, but we know very little about the roles of RNA end modification during RNA processing. We discovered that RNA end modification by the RNA 5´- kinase activity of the yeast tRNA ligase Trl1 is important to regulate the unfolded protein response by phosphorylating RNA intermediates during unintentional UPR activation to facilitate their turnover by 5´→3´ decay, and that Trl1 RNA 5´- kinase activity mediates the turnover of mRNA fragments created by co- translational “no-go” mRNA decay. The human RNA 5´-kinase enzyme Clp1 has an important role in neuronal metabolism and differentiation, but we do not know the substrates of Clp1 and so it is not clear how dysfunction in RNA 5´-kinase activity leads to disease. Our discovery that Trl1 5´-kinase activity mediates the decay of mRNA cleavage fragments also begs the question of whether the Trl1 ligase can also repair RNAs, but only a few examples of RNA repair are known. To address these issues, we will focus on the following questions: 1. What are the substrates of the human Clp1 RNA 5´-kinase?; 2. How do RNA end modification and processing regulate the unfolded protein response?; 3. How are the products of no-go mRNA decay created, and what are its physiological substrates?; 4. Is RNA repair restricted to specific substrates, or does it act on other damaged RNAs? The outcomes of these studies will be an improved understanding of how RNA end modification is used after RNA cleavage to mediate RNA processing, and these insights may inform our understanding of how dysfunction in RNA end modification underlies human disease.

Narrative During stress and normal growth, cells initiate programmed cleavage of RNAs by endonucleases to facilitate RNA processing. Several RNA end modification enzymes act on RNA cleavage products and have important roles in neuronal metabolism and differentiation, but we do not understand how the dysregulation RNA end modification causes disease. We will use new DNA sequencing-based methods as wells as genetic and biochemical approaches in yeast and human cells to address several unanswered questions about the roles of RNA end modification enzymes in cells, which will hopefully improve our understanding of their roles in RNA processing in cells, and may lead to new insights into their roles in human disease.